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Advances in biodiversity: metagenomics and the unveiling of biological dark matter

View Article: PubMed Central - PubMed

ABSTRACT

Background: Efforts to harmonize genomic data standards used by the biodiversity and metagenomic research communities have shown that prokaryotic data cannot be understood or represented in a traditional, classical biological context for conceptual reasons, not technical ones.

Results: Biology, like physics, has a fundamental duality—the classical macroscale eukaryotic realm vs. the quantum microscale microbial realm—with the two realms differing profoundly, and counter-intuitively, from one another. Just as classical physics is emergent from and cannot explain the microscale realm of quantum physics, so classical biology is emergent from and cannot explain the microscale realm of prokaryotic life. Classical biology describes the familiar, macroscale realm of multi-cellular eukaryotic organisms, which constitute a highly derived and constrained evolutionary subset of the biosphere, unrepresentative of the vast, mostly unseen, microbial world of prokaryotic life that comprises at least half of the planet’s biomass and most of its genetic diversity. The two realms occupy fundamentally different mega-niches: eukaryotes interact primarily mechanically with the environment, prokaryotes primarily physiologically. Further, many foundational tenets of classical biology simply do not apply to prokaryotic biology.

Conclusions: Classical genetics one held that genes, arranged on chromosomes like beads on a string, were the fundamental units of mutation, recombination, and heredity. Then, molecular analysis showed that there were no fundamental units, no beads, no string. Similarly, classical biology asserts that individual organisms and species are fundamental units of ecology, evolution, and biodiversity, composing an evolutionary history of objectively real, lineage-defined groups in a single-rooted tree of life. Now, metagenomic tools are forcing a recognition that there are no completely objective individuals, no unique lineages, and no one true tree. The newly revealed biosphere of microbial dark matter cannot be understood merely by extending the concepts and methods of eukaryotic macrobiology. The unveiling of biological dark matter is allowing us to see, for the first time, the diversity of the entire biosphere and, to paraphrase Darwin, is providing a new view of life. Advancing and understanding that view will require major revisions to some of the most fundamental concepts and theories in biology.

No MeSH data available.


The evolutionary relationships across all three domains of life, as reflected in the sequence similarity of their small subunit rRNA genes (after [68]). The differences among all the MCEs (inside the circle) is trivial, compared with the rest of the biosphere
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Fig2: The evolutionary relationships across all three domains of life, as reflected in the sequence similarity of their small subunit rRNA genes (after [68]). The differences among all the MCEs (inside the circle) is trivial, compared with the rest of the biosphere

Mentions: By the late 1990s, routine sequencing technology could use full, rather than indirect, measures of rRNA to construct evolutionary relationships among all life forms on Earth [68], or at least among their rRNA genes. In this universal tree (Fig. 2), with branch lengths proportional to rRNA sequence differences, all MCEs—animals, plants, and fungi—are encompassed within the small circle. From this perspective, all MCEs are a highly differentiated, specialized, and atypical form of life, no more representative of the entire biosphere than, say, hummingbirds are of the vertebrates.Fig. 2


Advances in biodiversity: metagenomics and the unveiling of biological dark matter
The evolutionary relationships across all three domains of life, as reflected in the sequence similarity of their small subunit rRNA genes (after [68]). The differences among all the MCEs (inside the circle) is trivial, compared with the rest of the biosphere
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5016886&req=5

Fig2: The evolutionary relationships across all three domains of life, as reflected in the sequence similarity of their small subunit rRNA genes (after [68]). The differences among all the MCEs (inside the circle) is trivial, compared with the rest of the biosphere
Mentions: By the late 1990s, routine sequencing technology could use full, rather than indirect, measures of rRNA to construct evolutionary relationships among all life forms on Earth [68], or at least among their rRNA genes. In this universal tree (Fig. 2), with branch lengths proportional to rRNA sequence differences, all MCEs—animals, plants, and fungi—are encompassed within the small circle. From this perspective, all MCEs are a highly differentiated, specialized, and atypical form of life, no more representative of the entire biosphere than, say, hummingbirds are of the vertebrates.Fig. 2

View Article: PubMed Central - PubMed

ABSTRACT

Background: Efforts to harmonize genomic data standards used by the biodiversity and metagenomic research communities have shown that prokaryotic data cannot be understood or represented in a traditional, classical biological context for conceptual reasons, not technical ones.

Results: Biology, like physics, has a fundamental duality—the classical macroscale eukaryotic realm vs. the quantum microscale microbial realm—with the two realms differing profoundly, and counter-intuitively, from one another. Just as classical physics is emergent from and cannot explain the microscale realm of quantum physics, so classical biology is emergent from and cannot explain the microscale realm of prokaryotic life. Classical biology describes the familiar, macroscale realm of multi-cellular eukaryotic organisms, which constitute a highly derived and constrained evolutionary subset of the biosphere, unrepresentative of the vast, mostly unseen, microbial world of prokaryotic life that comprises at least half of the planet’s biomass and most of its genetic diversity. The two realms occupy fundamentally different mega-niches: eukaryotes interact primarily mechanically with the environment, prokaryotes primarily physiologically. Further, many foundational tenets of classical biology simply do not apply to prokaryotic biology.

Conclusions: Classical genetics one held that genes, arranged on chromosomes like beads on a string, were the fundamental units of mutation, recombination, and heredity. Then, molecular analysis showed that there were no fundamental units, no beads, no string. Similarly, classical biology asserts that individual organisms and species are fundamental units of ecology, evolution, and biodiversity, composing an evolutionary history of objectively real, lineage-defined groups in a single-rooted tree of life. Now, metagenomic tools are forcing a recognition that there are no completely objective individuals, no unique lineages, and no one true tree. The newly revealed biosphere of microbial dark matter cannot be understood merely by extending the concepts and methods of eukaryotic macrobiology. The unveiling of biological dark matter is allowing us to see, for the first time, the diversity of the entire biosphere and, to paraphrase Darwin, is providing a new view of life. Advancing and understanding that view will require major revisions to some of the most fundamental concepts and theories in biology.

No MeSH data available.